Hi wondering if someone knows of a quick and easy way to offset a BAM alignment by N nucleotiodes towards the center of a fragment? Thank you.
-
-
I guess it depends on what you're trying to achieve. If you're trying to generate sharper coverage tracks then you can use bamCoverage from deepTools with either the --MNase or --centerReads options. Those both operate on fragments. -
Transposase
I am trying to account for the binding of Transposase by offsetting the read alignments on the +/- strands.
Originally posted by dpryan View PostComment
-
Provided you're happy with a bigWig file then either of the options I presented will work. Otherwise you might have to script something using pysam in python.Comment
-
I guess bamCoverage does not give the option to offset reads by specific numbers of bases given the binding event of specific enzymes?Comment
-
The current release doesn't offer this. However I happen to have a test branch that can do this (feature/riboseq_352). This was initially written with RiboSeq in mind, so there's a "--RiboSeq X" that will then use the Xth base from the 5' end of the read. I could change this to allow negative values, which would then support things like GROseq and PROseq. This is all in development, but it'll likely give reasonable results.Comment
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM
Comment